A Day Out at the University of Reading

Sabrina & Heather

At the end of June, Rose, head cheesemaker Heather, and Nicki and Karen from the office came to visit the labs at the University of Reading to see what I’ve been up to! My supervisor, Professor Glenn Gibson is soon retiring so it was a great opportunity for them to catch up with him. Here is what we got up to!

Head cheesemaker Heather, Nicki and Karen from the office, and Founder Rose.

Most of my experiments are run in the Food and Microbial Sciences Unit lab, here we run gut models (Figure 1) which mimic the conditions in the large intestine so we can research how different interventions can affect the gut microbiome. This model was designed by Glenn in 1998 and remains the

only gut model to be validated against the in vivo conditions of the human body; this was done by comparing the chemical and microbial conditions in the in vitro model with intestines of sudden-death victims. This type of validation is no longer possible due to regulations surrounding what human tissue can be used for, and so no other gut models produced can be validated in this way. This is a three stage model representing different sections of the colon; it is arranged vertically so the contents can flow down through the stages at a rate that mimics transit time through the colon. It is kept warm with a water bath, it is anaerobic by use of Nitrogen gas flow, the solution is kept agitated using magnetic stirrers, and the pH of each stage is monitored and controlled using a dilute solution of acid and alkali. The media that flows through is a mixture of different constituents, including protein and carbohydrate sources, that mimics the fluid that enters your large intestine from the ‘average’ Western diet (Figure 2). When the experiment is set up, each stage is inoculated with the faeces of a healthy person, and the system is left to equilibrate for two weeks. Once those two weeks are complete, we take samples across a few consecutive days to ensure that the model is stable, and then we can start the intervention. When I ran this experiment, I took cheese and put it through a process that simulates the earlier stages of digestion, including chewing, going through the stomach, and going through the small intestine. Then I can put this digested cheese into the top stage of the three-stage model and see how it changes the chemical and microbial environment of each of the three stages as it transitions through across two weeks, with a daily dose of cheese to represent consuming a portion of cheese every day. This experiment can be adapted to investigate

many different interventions, for example, herbal supplements or pharmaceuticals. You can also take faecal sample from different groups of people, e.g. newborn babies, autistic children, people with anxiety, or people with eating disorders, to analyse possible differences

in gut microbiome activity.

Figure 1 Glenn explaining the three-stage gut model

Figure 2 Two 5L bottle of media which will feed a pair of gut models for two weeks.

Figure 3 My lab coat hook in the FMSU lab!

Having seen (and smelt!) the gut model currently being run by my colleague, we had a look around the other labs in the department. Including the teaching labs where the undergraduate students are taught how to run food science experiments (Figure 4).

Figure 4 One of the food science teaching labs

We visited the flow cytometry lab; the bacterial analysis of the gut models often involves flow-FISH (fluorescent in situ hybridisation) cytometry. In this process, we take our samples and add DNA probes which will bind specifically to areas of DNA of certain groups of bacteria that we are interested in, these probes are attached to a fluorophore that will light up when exposed to a laser. We put our samples through the flow cytometer which involves passing the bacteria in a sample through an extremely narrow channel which only allows one cell through at a time and shines a laser beam across them (Figure 5). The laser will

light up the DNA probes, and the machine will measure the brightness of the light emitted and the way that it scatters across the detector. Using this, we can determine the quantity and types of bacteria in a sample.

Figure 5 Diagram of how flow cytometry works

In my experiments, I look at how the quantity of all bacteria and specific groups of bacteria changes in response to cheese in the gut models. The hypothesis is that the cheese will increase the number of probiotic bacteria in a sample, including Bifidobacteria and Lactococcus species. Some of the raw data from one of my experiments can be seen in Figures 6 and 7.

Figure 6 Looking at the raw data the cytometer produces

Figure 7 This set of graphs is showing the light scatter and graphical representation of the quantity of bacteria

Next, we took the group to see the Chemical Analysis Facility (CAF) (Figure 8). This is a lab in the Chemistry department which has all manner of interesting analytical equipment. In my studies so far I have used the nuclear magnetic resonance (NMR) spectrometer to look at the presence of different compounds in my samples (Figure 9). This machine uses a very strong magnet which excites any hydrogen atoms in a sample and then detects the signals that these atoms give out in response. Different compounds will return different signals, so

we can use the spectra that the NMR spectrometer produces to work out which compounds are present in a sample. For example, Figure 10 shows the spectra produced when I compared young vs mature Bix!

Figure 8 The 700MHz NMR spectrometer

We finished the visit with lunch at the on-campus pub! It was super fun to show some of the Creamery team around the labs and explain what I have been doing, I think they enjoyed it too!